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Apple made some overnight change to the AppStore in iTunes which appears to be an attempt to better organize and showcase the 10,000 applications.

Top free and top paid applications are now separated. They are both positioned in the right column of the AppStore with paid apps above the free apps. This change was probably made to help feature paid apps more -- the previous top apps section of proliferated by free apps. Follow the source links at the bottom. Looks like they actually moved Free and Paid to the right and left in category views instead of both in the right column. Sadly not in my iTunes but ohwell. Update: Now the new layout is showing up -- pic updated.

The other change made was now the top 100 apps are shown instead of the top 50. Good apps that are out of the top 50 (yes there are some) will now more noticeable possibly promoting more downloads/sales.

While the AppStore still isn't excellent at featuring everything it looks like Apple is making efforts to to improve. You might note that similar changes were already made on the iPhone version of the AppStore back with the latest update to version 2.2 so the changes made in the AppStore via iTunes probably is not in response to complaints by developers concerning the AppStore. This is just something that was probably already on Apple's list and was finally implemented.